GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Sphingomonas koreensis DSMZ 15582

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Ga0059261_2519 Ga0059261_2519 aspartate kinase (EC 2.7.2.4)

Query= BRENDA::O69077
         (412 letters)



>FitnessBrowser__Korea:Ga0059261_2519
          Length = 419

 Score =  414 bits (1064), Expect = e-120
 Identities = 229/414 (55%), Positives = 291/414 (70%), Gaps = 7/414 (1%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           MA IV KFGGTS+  +ERI  VA +VK   EAG+ V VVVSAM+GET+RL+G   +    
Sbjct: 1   MARIVMKFGGTSMAGIERIRNVANRVKAEWEAGNQVAVVVSAMAGETDRLVGFCREASPL 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
              RE D +VS GEQVT  LL++AL   GVPA S+ G Q+ I T SAH  ARI  ID T 
Sbjct: 61  YDLREYDTVVSAGEQVTSGLLAIALQAIGVPARSWLGWQLPIHTSSAHASARIGTIDTTE 120

Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           + A L  G V V+ GFQG+  +  +TTLGRGGSDT+ VA+AAA+KAD C IYTDVDGVYT
Sbjct: 121 LNASLADGNVAVIPGFQGLAEDNRVTTLGRGGSDTSAVAVAAAMKADRCDIYTDVDGVYT 180

Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEG----- 235
           TDPR+VP+AR+L K+T+EEMLE+AS+G+KVLQ R+V  A K  V +RVL S ++      
Sbjct: 181 TDPRIVPRARKLSKVTYEEMLELASVGAKVLQTRSVGLAMKEGVRVRVLSSLEDNRDEEG 240

Query: 236 -PGTLITIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDM 294
             GTLI  ++E   +E+ +I+GIA +++EAK+T+  VPD PG    I  P++ A + VDM
Sbjct: 241 HRGTLIVGEEEINDVERQLITGIAADKNEAKVTLTNVPDRPGAVGHIFTPLAEAGINVDM 300

Query: 295 IVQNVAH-DNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRS 353
           IVQNVAH   +TD TFTV R +   AL++L+++ A IG    I DT +AK+S+VGVGMRS
Sbjct: 301 IVQNVAHATGSTDVTFTVPRAELARALDVLEKSKAPIGYDALIHDTKVAKISVVGVGMRS 360

Query: 354 HAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAP 407
           HAGVA+ MFE L +  INI  I+TSEIKVSV+I E   ELAVR LHTA+ LDAP
Sbjct: 361 HAGVAATMFETLGERRINILAITTSEIKVSVLIHEDETELAVRVLHTAYGLDAP 414


Lambda     K      H
   0.317    0.133    0.362 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 468
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 412
Length of database: 419
Length adjustment: 31
Effective length of query: 381
Effective length of database: 388
Effective search space:   147828
Effective search space used:   147828
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate Ga0059261_2519 Ga0059261_2519 (aspartate kinase (EC 2.7.2.4))
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00657.hmm
# target sequence database:        /tmp/gapView.10171.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate kinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-132  427.9   8.1   4.2e-111  358.1   3.5    2.0  2  lcl|FitnessBrowser__Korea:Ga0059261_2519  Ga0059261_2519 aspartate kinase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2519  Ga0059261_2519 aspartate kinase (EC 2.7.2.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.1   1.8e-24   1.8e-24       1      59 [.       1      59 [.       1      62 [. 0.97
   2 !  358.1   3.5  4.2e-111  4.2e-111     104     440 ..      64     409 ..      60     411 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.8e-24
                                 TIGR00657  1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvss 59
                                              ma+iV+KFGGtS++ +eri++va++vk+e e gnqv+VVvSAmag Td+Lv +++++s+
  lcl|FitnessBrowser__Korea:Ga0059261_2519  1 MARIVMKFGGTSMAGIERIRNVANRVKAEWEAGNQVAVVVSAMAGETDRLVGFCREASP 59
                                              799****************************************************9986 PP

  == domain 2  score: 358.1 bits;  conditional E-value: 4.2e-111
                                 TIGR00657 104 reldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiiv 172
                                               re+d+++s GE++++ lla al++ gv a+s+lg++ +i t+s++ +A+ + +i+t +l++ l  g + 
  lcl|FitnessBrowser__Korea:Ga0059261_2519  64 REYDTVVSAGEQVTSGLLAIALQAIGVPARSWLGWQLPIHTSSAHASAR-IGTIDTTELNASLADGNVA 131
                                               89***********************************************.******************* PP

                                 TIGR00657 173 vvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEa 241
                                               v+ GF+G+ e++++ttLGRGGSD++A+++Aaa+kAd+++iytDVdG+yt+DPrivp Ar+l +++yeE+
  lcl|FitnessBrowser__Korea:Ga0059261_2519 132 VIPGFQGLAEDNRVTTLGRGGSDTSAVAVAAAMKADRCDIYTDVDGVYTTDPRIVPRARKLSKVTYEEM 200
                                               ********************************************************************* PP

                                 TIGR00657 242 lELaslGakvLhprtlepamrakipivvkstfnpe.....aeGTlivaksk..seeepavkalsldknq 303
                                               lELas+GakvL+ r++ +am+ +++++v s+ +++       GTliv++++  + e++ +++++ dkn+
  lcl|FitnessBrowser__Korea:Ga0059261_2519 201 LELASVGAKVLQTRSVGLAMKEGVRVRVLSSLEDNrdeegHRGTLIVGEEEinDVERQLITGIAADKNE 269
                                               ****************************999876522222469******9998667799********** PP

                                 TIGR00657 304 alvsvsgttmkpgilaevfgalaeakvnvdlilqsssets....isfvvdkedadkakellkkkvkeek 368
                                               a+v++  ++++pg + ++f+ laea++nvd+i+q++ + +    ++f+v++ ++ +a  +l +k k+  
  lcl|FitnessBrowser__Korea:Ga0059261_2519 270 AKVTLTNVPDRPGAVGHIFTPLAEAGINVDMIVQNVAHATgstdVTFTVPRAELARALDVL-EKSKAPI 337
                                               ***********************************994444678****************8.5699999 PP

                                 TIGR00657 369 aleevevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealh 437
                                                   +  ++k+a++s+vG gm+s+ gvaa++fe+L e+ ini +i +seik+sv+++e++ e av++lh
  lcl|FitnessBrowser__Korea:Ga0059261_2519 338 GYDALIHDTKVAKISVVGVGMRSHAGVAATMFETLGERRINILAITTSEIKVSVLIHEDETELAVRVLH 406
                                               ********************************************************************* PP

                                 TIGR00657 438 ekl 440
                                                ++
  lcl|FitnessBrowser__Korea:Ga0059261_2519 407 TAY 409
                                               998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (419 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 4.29
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory